Serverification of Molecular Modeling Applications: The Rosetta Online Server That Includes Everyone (ROSIE)

Sergey Lyskov, Fang Chieh Chou, Shane Ó Conchúir, Bryan S. Der, Kevin Drew, Daisuke Kuroda, Jianqing Xu, Brian D. Weitzner, P. Douglas Renfrew, Parin Sripakdeevong, Benjamin Borgo, James J. Havranek, Brian Kuhlman, Tanja Kortemme, Richard Bonneau, Jeffrey J. Gray, Rhiju Das

Research output: Contribution to journalArticle

Abstract

The Rosetta molecular modeling software package provides experimentally tested and rapidly evolving tools for the 3D structure prediction and high-resolution design of proteins, nucleic acids, and a growing number of non-natural polymers. Despite its free availability to academic users and improving documentation, use of Rosetta has largely remained confined to developers and their immediate collaborators due to the code's difficulty of use, the requirement for large computational resources, and the unavailability of servers for most of the Rosetta applications. Here, we present a unified web framework for Rosetta applications called ROSIE (Rosetta Online Server that Includes Everyone). ROSIE provides (a) a common user interface for Rosetta protocols, (b) a stable application programming interface for developers to add additional protocols, (c) a flexible back-end to allow leveraging of computer cluster resources shared by RosettaCommons member institutions, and (d) centralized administration by the RosettaCommons to ensure continuous maintenance. This paper describes the ROSIE server infrastructure, a step-by-step 'serverification' protocol for use by Rosetta developers, and the deployment of the first nine ROSIE applications by six separate developer teams: Docking, RNA de novo, ERRASER, Antibody, Sequence Tolerance, Supercharge, Beta peptide design, NCBB design, and VIP redesign. As illustrated by the number and diversity of these applications, ROSIE offers a general and speedy paradigm for serverification of Rosetta applications that incurs negligible cost to developers and lowers barriers to Rosetta use for the broader biological community. ROSIE is available at http://rosie.rosettacommons.org.

Original languageEnglish (US)
Article numbere63906
JournalPloS one
Volume8
Issue number5
DOIs
StatePublished - May 22 2013

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ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

Cite this

Lyskov, S., Chou, F. C., Conchúir, S. Ó., Der, B. S., Drew, K., Kuroda, D., Xu, J., Weitzner, B. D., Renfrew, P. D., Sripakdeevong, P., Borgo, B., Havranek, J. J., Kuhlman, B., Kortemme, T., Bonneau, R., Gray, J. J., & Das, R. (2013). Serverification of Molecular Modeling Applications: The Rosetta Online Server That Includes Everyone (ROSIE). PloS one, 8(5), [e63906]. https://doi.org/10.1371/journal.pone.0063906